The process of kidney failure in renal transplant recipients with chronic allograft dysfunction is characterized by a progressive decline in glomerular filtration rate over time that it is determined by the 5-stage model. This study used stage-based statistical survival analysis to predict graft survival in renal transplant recipients with chronic allograft dysfunction. In a single-center, retrospective study, 214 renal transplant recipients with chronic allograft dysfunction were investigated at a university hospital in Iran from 1997 to 2005. At each patient visit, kidney function was assessed using glomerular filtration rate and stage of disease. The estimated stage-specific hazard rates of disease progression are stage one, 453.936; stage two, 485.040; stage three, 545.808; and stage four; 649.488 per 1000 person-years. The estimated mean times in each stage were as follows: kidney damage with normal or increased glomerular filtration rate, 26.43 months; kidney damage with mildly decreased glomerular filtration rate, 24.74 months; moderate kidney disease, 21.98 months; and severe kidney disease; 18.48 months. These estimates yield a mean time from stage 1 to kidney failure of 91.63 months. The probability of graft survival was predicted using estimated stage-specific hazard rates. The 18th, 58th, 118th, and 155th months death-censored graft survival probabilities were 0.99, 0.75, 0.25, and 0.10. In this method of survival analysis, we can determine a statistical model according to a real clinical model in renal transplant recipients with chronic allograft dysfunction. It enables us to determine the stage-specific hazard rates of disease progression. These findings can help nephrologists to understand the kidney disease process and better predict graft survival.